# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:45:54 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(c(CC2CC2)n1)c3ccnc(Nc4ccncc4)n3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2UG  2UG  4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine  ligand  41  24  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2UG
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2UG  C1   C  CR16  0  -0.028   3.1462   1.7689  -0.3821
 2UG  C2   C  CR6   0  -0.112   2.2000   0.8847   0.1348
 2UG  C3   C  CR6   0   0.246   0.8087   1.3256   0.2762
 2UG  C11  C  CR16  0  -0.377  -4.5202   1.0420   0.1690
 2UG  C12  C  CR6   0   0.331   2.6913  -0.3854   0.4878
 2UG  C13  C  CH2   0  -0.538   1.8548  -1.4818   1.0827
 2UG  C14  C  CH1   0  -0.232   1.3420  -2.4306   0.0213
 2UG  C15  C  CH2   0  -0.479   2.2572  -3.4526  -0.5742
 2UG  C16  C  CH2   0  -0.497   1.1550  -3.8800   0.3492
 2UG  C    C  CR6   0   0.553   4.7819   0.2380  -0.2006
 2UG  N6   N  N     0  -0.461   3.9696  -0.6840   0.3245
 2UG  N1   N  N     0  -0.453   4.4151   1.4749  -0.5642
 2UG  N5   N  N     0  -0.483  -0.1592   0.4603   0.0089
 2UG  C6   C  CR6   0   0.611  -1.4182   0.8802   0.1232
 2UG  N2   N  N     0  -0.463  -1.8082   2.0979   0.4686
 2UG  C5   C  CR16  0   0.007  -0.8337   2.9615   0.7336
 2UG  C4   C  CR16  0  -0.396   0.5032   2.6353   0.6625
 2UG  N3   N  NH1   0  -0.772  -2.3463  -0.0830  -0.1688
 2UG  C7   C  CR6   0   0.454  -3.7221  -0.0508  -0.1804
 2UG  C10  C  CR16  0  -0.072  -5.8968   0.8990   0.1038
 2UG  N4   N  N     0  -0.424  -6.5324  -0.2053  -0.2684
 2UG  C9   C  CR16  0  -0.066  -5.7646  -1.2411  -0.5991
 2UG  C8   C  CR16  0  -0.424  -4.3858  -1.2204  -0.5737
 2UG  H1   H  HCR6  0   0.271   2.8423   2.7659  -0.6868
 2UG  H2   H  HCR6  0   0.293  -4.0913   1.9779   0.4841
 2UG  H3   H  HCH2  0   0.254   2.4869  -2.0313   1.7843
 2UG  H4   H  HCH2  0   0.254   1.0154  -1.0767   1.6467
 2UG  H5   H  HCH1  0   0.262   0.6108  -1.9881  -0.6449
 2UG  H6   H  HCH2  0   0.245   2.1593  -3.6748  -1.6293
 2UG  H7   H  HCH2  0   0.243   3.2745  -3.4923  -0.2058
 2UG  H8   H  HCH2  0   0.242   1.4272  -4.2170   1.3424
 2UG  H9   H  HCH2  0   0.247   0.2994  -4.3928  -0.0716
 2UG  H10  H  HNH2  0   0.402   6.3732  -1.0347  -0.1819
 2UG  H11  H  HNH2  0   0.402   6.7025   0.5396  -0.8121
 2UG  H12  H  HCR6  0   0.278  -1.1425   3.9588   1.0249
 2UG  H13  H  HCR6  0   0.278   1.2660   3.3566   0.9148
 2UG  H14  H  HNH1  0   0.413  -1.9293  -0.9630  -0.4351
 2UG  H15  H  HCR6  0   0.261  -6.5196   1.7451   0.3752
 2UG  H16  H  HCR6  0   0.263  -6.2752  -2.1474  -0.9059
 2UG  H17  H  HCR6  0   0.280  -3.8294  -2.1042  -0.8597
 2UG  N    N  NH2   0  -0.816   6.0694  -0.0929  -0.3556

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2UG  C5   N2   aromatic  1.329  0.020  1.329
 2UG  C5   C4   aromatic  1.378  0.020  1.378
 2UG  N2   C6   aromatic  1.325  0.020  1.325
 2UG  C4   C3   aromatic  1.399  0.020  1.399
 2UG  C6   N3   single    1.369  0.020  1.369
 2UG  C6   N5   aromatic  1.332  0.020  1.332
 2UG  N3   C7   single    1.376  0.020  1.376
 2UG  C3   N5   aromatic  1.325  0.020  1.325
 2UG  C3   C2   single    1.466  0.020  1.466
 2UG  C1   C2   aromatic  1.394  0.020  1.394
 2UG  C1   N1   aromatic  1.315  0.020  1.315
 2UG  C11  C7   aromatic  1.398  0.020  1.398
 2UG  C11  C10  aromatic  1.386  0.020  1.386
 2UG  C7   C8   aromatic  1.401  0.020  1.401
 2UG  C2   C12  aromatic  1.407  0.020  1.407
 2UG  N1   C    aromatic  1.340  0.020  1.340
 2UG  C10  N4   aromatic  1.327  0.020  1.327
 2UG  C8   C9   aromatic  1.379  0.020  1.379
 2UG  C12  C13  single    1.502  0.020  1.502
 2UG  C12  N6   aromatic  1.323  0.020  1.323
 2UG  C    N6   aromatic  1.336  0.020  1.336
 2UG  C    N    single    1.338  0.020  1.338
 2UG  C13  C14  single    1.513  0.020  1.513
 2UG  C14  C16  single    1.498  0.020  1.498
 2UG  C14  C15  single    1.496  0.020  1.496
 2UG  N4   C9   aromatic  1.331  0.020  1.331
 2UG  C16  C15  single    1.500  0.020  1.500
 2UG  C1   H1   single    0.930  0.020  1.080
 2UG  C11  H2   single    0.930  0.020  1.080
 2UG  C13  H3   single    0.970  0.020  1.090
 2UG  C13  H4   single    0.970  0.020  1.090
 2UG  C14  H5   single    0.970  0.020  1.090
 2UG  C15  H6   single    0.970  0.020  1.090
 2UG  C15  H7   single    0.970  0.020  1.090
 2UG  C16  H8   single    0.970  0.020  1.090
 2UG  C16  H9   single    0.970  0.020  1.090
 2UG  N    H10  single    0.860  0.020  1.020
 2UG  N    H11  single    0.860  0.020  1.020
 2UG  C5   H12  single    0.930  0.020  1.080
 2UG  C4   H13  single    0.930  0.020  1.080
 2UG  N3   H14  single    0.860  0.020  1.020
 2UG  C10  H15  single    0.930  0.020  1.080
 2UG  C9   H16  single    0.930  0.020  1.080
 2UG  C8   H17  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 2UG  H1   C1   N1   115.88  3.000
 2UG  H1   C1   C2   119.76  3.000
 2UG  N1   C1   C2   124.35  3.000
 2UG  C12  C2   C3   125.36  3.000
 2UG  C12  C2   C1   115.37  3.000
 2UG  C3   C2   C1   119.27  3.000
 2UG  C4   C3   N5   120.48  3.000
 2UG  N5   C3   C2   118.50  3.000
 2UG  C4   C3   C2   121.01  3.000
 2UG  H2   C11  C10  119.95  3.000
 2UG  H2   C11  C7   121.70  3.000
 2UG  C10  C11  C7   118.35  3.000
 2UG  N6   C12  C13  114.98  3.000
 2UG  N6   C12  C2   120.68  3.000
 2UG  C13  C12  C2   124.33  3.000
 2UG  H4   C13  H3   107.48  3.000
 2UG  H4   C13  C14  109.58  3.000
 2UG  H3   C13  C14  109.33  3.000
 2UG  H4   C13  C12  111.27  3.000
 2UG  H3   C13  C12  107.42  3.000
 2UG  C14  C13  C12  111.63  3.000
 2UG  H5   C14  C16  116.45  3.000
 2UG  H5   C14  C15  116.56  3.000
 2UG  C16  C14  C15   60.15  3.000
 2UG  H5   C14  C13  113.82  3.000
 2UG  C15  C14  C13  120.02  3.000
 2UG  C16  C14  C13  119.70  3.000
 2UG  H7   C15  H6   114.15  3.000
 2UG  H7   C15  C16  118.07  3.000
 2UG  H6   C15  C16  118.36  3.000
 2UG  H7   C15  C14  117.68  3.000
 2UG  H6   C15  C14  118.22  3.000
 2UG  C16  C15  C14   60.00  3.000
 2UG  H9   C16  H8   114.04  3.000
 2UG  H9   C16  C15  118.45  3.000
 2UG  H8   C16  C15  117.92  3.000
 2UG  H9   C16  C14  118.16  3.000
 2UG  H8   C16  C14  118.05  3.000
 2UG  C15  C16  C14   59.85  3.000
 2UG  N1   C    N6   125.24  3.000
 2UG  N6   C    N    117.37  3.000
 2UG  N1   C    N    117.39  3.000
 2UG  C    N6   C12  118.70  3.000
 2UG  C    N1   C1   115.65  3.000
 2UG  C6   N5   C3   117.85  3.000
 2UG  N3   C6   N2   120.19  3.000
 2UG  N3   C6   N5   113.62  3.000
 2UG  N2   C6   N5   126.19  3.000
 2UG  C5   N2   C6   115.70  3.000
 2UG  H12  C5   C4   120.54  3.000
 2UG  H12  C5   N2   116.28  3.000
 2UG  C4   C5   N2   123.18  3.000
 2UG  H13  C4   C5   121.01  3.000
 2UG  H13  C4   C3   122.38  3.000
 2UG  C5   C4   C3   116.59  3.000
 2UG  H14  N3   C7   115.53  3.000
 2UG  H14  N3   C6   112.93  3.000
 2UG  C7   N3   C6   131.53  3.000
 2UG  C8   C7   N3   117.16  3.000
 2UG  C8   C7   C11  116.90  3.000
 2UG  N3   C7   C11  125.94  3.000
 2UG  H15  C10  N4   116.36  3.000
 2UG  H15  C10  C11  118.56  3.000
 2UG  N4   C10  C11  125.08  3.000
 2UG  C9   N4   C10  116.16  3.000
 2UG  H16  C9   C8   119.24  3.000
 2UG  H16  C9   N4   116.68  3.000
 2UG  C8   C9   N4   124.08  3.000
 2UG  H17  C8   C9   119.78  3.000
 2UG  H17  C8   C7   120.80  3.000
 2UG  C9   C8   C7   119.42  3.000
 2UG  H11  N    H10  118.57  3.000
 2UG  H11  N    C    120.21  3.000
 2UG  H10  N    C    120.18  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 2UG  CONST_03  N6   C12  C2   C1      0.00   0.0  0
 2UG  CONST_04  N6   C    N1   C1      0.00   0.0  0
 2UG  CONST_05  C5   C4   C3   C2    180.00   0.0  0
 2UG  CONST_06  C6   N5   C3   C2    180.00   0.0  0
 2UG  CONST_07  C    N1   C1   C2      0.00   0.0  0
 2UG  CONST_08  C    N6   C12  C2      0.00   0.0  0
 2UG  CONST_09  N2   C5   C4   C3      0.00   0.0  0
 2UG  CONST_10  N2   C6   N5   C3      0.00   0.0  0
 2UG  CONST_11  N1   C1   C2   C3    180.00   0.0  0
 2UG  CONST_12  N6   C12  C2   C3    180.00   0.0  0
 2UG  CONST_13  C9   C8   C7   C11     0.00   0.0  0
 2UG  CONST_14  C9   N4   C10  C11     0.00   0.0  0
 2UG  CONST_17  N1   C1   C2   C12     0.00   0.0  0
 2UG  CONST_18  N1   C    N6   C12     0.00   0.0  0
 2UG  CONST_19  C5   N2   C6   N5      0.00   0.0  0
 2UG  CONST_20  C5   C4   C3   N5      0.00   0.0  0
 2UG  CONST_21  C4   C5   N2   C6      0.00   0.0  0
 2UG  CONST_22  C4   C3   N5   C6      0.00   0.0  0
 2UG  CONST_23  N4   C10  C11  C7      0.00   0.0  0
 2UG  CONST_24  N4   C9   C8   C7      0.00   0.0  0
 2UG  CONST_25  C8   C7   C11  C10     0.00   0.0  0
 2UG  CONST_26  C8   C9   N4   C10     0.00   0.0  0
 2UG  CONST_27  C13  C12  C2   C1    180.00   0.0  0
 2UG  CONST_28  N    C    N1   C1    180.00   0.0  0
 2UG  CONST_29  N3   C6   N5   C3    180.00   0.0  0
 2UG  CONST_30  C13  C12  C2   C3      0.00   0.0  0
 2UG  CONST_31  N    C    N6   C12   180.00   0.0  0
 2UG  CONST_32  C    N6   C12  C13   180.00   0.0  0
 2UG  CONST_33  N3   C6   N2   C5    180.00   0.0  0
 2UG  CONST_34  C10  C11  C7   N3    180.00   0.0  0
 2UG  CONST_35  C9   C8   C7   N3    180.00   0.0  0
 2UG  CONST_36  H13  C4   C3   C2      0.00   0.0  0
 2UG  CONST_37  H12  C5   C4   C3    180.00   0.0  0
 2UG  CONST_38  H1   C1   C2   C3      0.00   0.0  0
 2UG  CONST_39  H17  C8   C7   C11   180.00   0.0  0
 2UG  CONST_40  H15  C10  C11  C7    180.00   0.0  0
 2UG  CONST_41  H16  C9   C8   C7    180.00   0.0  0
 2UG  CONST_42  H2   C11  C10  N4    180.00   0.0  0
 2UG  CONST_43  H10  N    C    N6      0.00   0.0  0
 2UG  CONST_44  H11  N    C    N6    180.00   0.0  0
 2UG  Var_01    C14  C13  C12  C2     94.77  30.0  2
 2UG  Var_02    C6   N3   C7   C11    -2.25  30.0  3
 2UG  Var_03    C16  C14  C13  C12   147.37  30.0  3
 2UG  Var_04    C15  C16  C14  C13  -109.68  30.0  1
 2UG  Var_05    C7   N3   C6   N5   -179.44  30.0  2
 2UG  Var_06    H6   C15  C16  C14  -107.99  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2UG  chir_01  C14  C13  C16  C15  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2UG  plan-1  C1   0.020
 2UG  plan-1  C2   0.020
 2UG  plan-1  C3   0.020
 2UG  plan-1  C12  0.020
 2UG  plan-1  C13  0.020
 2UG  plan-1  C    0.020
 2UG  plan-1  N6   0.020
 2UG  plan-1  N1   0.020
 2UG  plan-1  H1   0.020
 2UG  plan-1  N    0.020
 2UG  plan-2  C11  0.020
 2UG  plan-2  N3   0.020
 2UG  plan-2  C7   0.020
 2UG  plan-2  C10  0.020
 2UG  plan-2  N4   0.020
 2UG  plan-2  C9   0.020
 2UG  plan-2  C8   0.020
 2UG  plan-2  H2   0.020
 2UG  plan-2  H15  0.020
 2UG  plan-2  H16  0.020
 2UG  plan-2  H17  0.020
 2UG  plan-3  C2   0.020
 2UG  plan-3  C3   0.020
 2UG  plan-3  N5   0.020
 2UG  plan-3  C6   0.020
 2UG  plan-3  N2   0.020
 2UG  plan-3  C5   0.020
 2UG  plan-3  C4   0.020
 2UG  plan-3  N3   0.020
 2UG  plan-3  H12  0.020
 2UG  plan-3  H13  0.020
 2UG  plan-4  C    0.020
 2UG  plan-4  H10  0.020
 2UG  plan-4  H11  0.020
 2UG  plan-4  N    0.020

